Alright, so I have been trying for some time now. But it seems that most programs except Paint.net (and maybe Gimp) doesnt like transparency in VTF files. They open up and look extremely weird. I even tried opening a normal PNG with transparency in it with VTFlib, but still it doesnt seem like it have any transparency in it.
Photoshop looks like this:
It’s really starting to piss me off a lot, as I have used a long time on trying to make it work.
Here’s a screen of VTFlib: